Nature Microbiology最新文献_第3页

Author Correction: Aspergillus cvjetkovicii protects against phytopathogens through interspecies chemical signalling in the phyllosphere

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-31 DOI: 10.1038/s41564-025-01942-8

Xiaoyan Fan, Haruna Matsumoto, Haorong Xu, Hongda Fang, Qianqian Pan, Tianxing Lv, Chengfang Zhan, Xiaoxiao Feng, Xiaoyu Liu, Danrui Su, Mengyuan Fan, Zhonghua Ma, Gabriele Berg, Shaojia Li, Tomislav Cernava, Mengcen Wang

引用次数: 0

Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-31 DOI: 10.1038/s41564-025-01931-x

Linxing Li, Yutao Liu, Dan Liu, Jing Wang, Min Wang, Binbin Xiang, Jingliang Qin, Ting Yao, Wanwu Li, Pan Wu, Qian Wang, Jianji Zhang, Yanli Xu, Miaomiao Liu, Yanling Wang, Guozhen Ma, Ruiying Liu, Xiaoya Li, Zimeng Huai, Yu Huang, Han Guo, Bin Yang, Lu Feng, Di Huang, Kai Zhang, Lei Wang, Bin Liu

{"title":"Microbiota-derived succinate promotes enterohaemorrhagic Escherichia coli virulence via lysine succinylation","authors":"Linxing Li, Yutao Liu, Dan Liu, Jing Wang, Min Wang, Binbin Xiang, Jingliang Qin, Ting Yao, Wanwu Li, Pan Wu, Qian Wang, Jianji Zhang, Yanli Xu, Miaomiao Liu, Yanling Wang, Guozhen Ma, Ruiying Liu, Xiaoya Li, Zimeng Huai, Yu Huang, Han Guo, Bin Yang, Lu Feng, Di Huang, Kai Zhang, Lei Wang, Bin Liu","doi":"10.1038/s41564-025-01931-x","DOIUrl":"https://doi.org/10.1038/s41564-025-01931-x","url":null,"abstract":"Succinate upregulates enterohaemorrhagic Escherichia coli (EHEC) virulence. Lysine succinylation, a post-translational modification, regulates cellular function in eukaryotes but is less characterized in bacteria. We hypothesized that lysine succinylation regulates EHEC virulence. Here we used SILAC-based proteomics and characterized the EHEC succinylome to show that the transcription factor, PurR, is succinylated at K24 and K55. Succinylation of PurR inhibited its ability to directly bind DNA and repress expression of a major virulence factor, the Type 3 Secretion System (T3SS), thus increasing T3SS expression. Deletion of purR, or K24E or K55E mutation, increased EHEC adherence to cells and colonization of infant rabbits. Using mice treated with streptomycin to deplete succinate, or colonized with succinate-producing Prevotella copri to increase succinate levels, we showed that microbiota-derived succinate increased succinylation of PurR to promote virulence of Citrobacter rodentium, a model for EHEC, in mice. Lastly, we identified CitC as the succinyltransferase required for PurR modification.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"84 1","pages":""},"PeriodicalIF":28.3,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071897","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-31 DOI: 10.1038/s41564-024-01911-7

Cassie R. Bakshani, Taiwo O. Ojuri, Bo Pilgaard, Jesper Holck, Ross McInnes, Radoslaw P. Kozak, Maria Zakhour, Sara Çakaj, Manon Kerouedan, Emily Newton, David N. Bolam, Lucy I. Crouch

{"title":"Carbohydrate-active enzymes from Akkermansia muciniphila break down mucin O-glycans to completion","authors":"Cassie R. Bakshani, Taiwo O. Ojuri, Bo Pilgaard, Jesper Holck, Ross McInnes, Radoslaw P. Kozak, Maria Zakhour, Sara Çakaj, Manon Kerouedan, Emily Newton, David N. Bolam, Lucy I. Crouch","doi":"10.1038/s41564-024-01911-7","DOIUrl":"10.1038/s41564-024-01911-7","url":null,"abstract":"Akkermansia muciniphila is a human microbial symbiont residing in the mucosal layer of the large intestine. Its main carbon source is the highly heterogeneous mucin glycoprotein, and it uses an array of carbohydrate-active enzymes and sulfatases to access this complex energy source. Here we describe the biochemical characterization of 54 glycoside hydrolases, 11 sulfatases and 1 polysaccharide lyase from A. muciniphila to provide a holistic understanding of their carbohydrate-degrading activities. This was achieved using a variety of liquid chromatography techniques, mass spectrometry, enzyme kinetics and thin-layer chromatography. These results are supported with A. muciniphila growth and whole-cell assays. We find that these enzymes can act synergistically to degrade the O-glycans on the mucin polypeptide to completion, down to the core N-acetylgalactosaime. In addition, these enzymes can break down human breast milk oligosaccharide, ganglioside and globoside glycan structures, showing their capacity to target a variety of host glycans. These data provide a resource to understand the full degradative capability of the gut microbiome member A. muciniphila. Biochemical characterization of 66 carbohydrate-active enzymes from the gut microorganism Akkermansia muciniphila reveals that these enzymes can break down a range of host glycans, including mucin, which they degrade to completion.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"585-598"},"PeriodicalIF":20.5,"publicationDate":"2025-01-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01911-7.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143071960","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Engineering mycobacteria for vaccination and controlled human infection studies

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-27 DOI: 10.1038/s41564-024-01923-3

Erin F. McCaffrey, Daniel L. Barber

引用次数: 0

Integrons are anti-phage defence libraries in Vibrio parahaemolyticus

IF 28.3 1区生物学

Nature Microbiology Pub Date : 2025-01-27 DOI: 10.1038/s41564-025-01927-7

Landon J. Getz, Sam R. Fairburn, Y. Vivian Liu, Amy L. Qian, Karen L. Maxwell

引用次数: 0

Longitudinal phage–bacteria dynamics in the early life gut microbiome

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01906-4

Michael J. Tisza, Richard E. Lloyd, Kristi Hoffman, Daniel P. Smith, Marian Rewers, Sara J. Javornik Cregeen, Joseph F. Petrosino

{"title":"Longitudinal phage–bacteria dynamics in the early life gut microbiome","authors":"Michael J. Tisza, Richard E. Lloyd, Kristi Hoffman, Daniel P. Smith, Marian Rewers, Sara J. Javornik Cregeen, Joseph F. Petrosino","doi":"10.1038/s41564-024-01906-4","DOIUrl":"10.1038/s41564-024-01906-4","url":null,"abstract":"Microbial colonization of the human gut occurs soon after birth, proceeds through well-studied phases and is affected by lifestyle and other factors. Less is known about phage community dynamics during infant gut colonization due to small study sizes, an inability to leverage large databases and a lack of appropriate bioinformatics tools. Here we reanalysed whole microbial community shotgun sequencing data of 12,262 longitudinal samples from 887 children from four countries across four years of life as part of the The Environmental Determinants of Diabetes in the Young (TEDDY) study. We developed an extensive metagenome-assembled genome catalogue using the Marker-MAGu pipeline, which comprised 49,111 phage taxa from existing human microbiome datasets. This was used to identify phage marker genes and their integration into the MetaPhlAn 4 bacterial marker gene database enabled simultaneous assessment of phage and bacterial dynamics. We found that individual children are colonized by hundreds of different phages, which are more transitory than bacteria, accumulating a more diverse phage community over time. Type 1 diabetes correlated with a decreased rate of change in bacterial and viral communities in children aged one and two. The addition of phage data improved the ability of machine learning models to discriminate samples by country. Finally, although phage populations were specific to individuals, we observed trends of phage ecological succession that correlated well with putative host bacteria. This resource improves our understanding of phage–bacteria interactions in the developing early life microbiome. Reanalysis of 12,262 longitudinal infant gut microbiome samples using the Marker-MAGu pipeline revealed phage–bacteria dynamics over the first year of life.","PeriodicalId":18992,"journal":{"name":"Nature Microbiology","volume":"10 2","pages":"420-430"},"PeriodicalIF":20.5,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.nature.com/articles/s41564-024-01906-4.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143026713","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"生物学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Explainable artificial intelligence evolves antimicrobial peptides

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01919-z

Jeremie Alexander, Gary Liu, Jonathan M. Stokes

引用次数: 0

A gut microorganism turns the dial on sugar intake

IF 20.5 1区生物学

Nature Microbiology Pub Date : 2025-01-24 DOI: 10.1038/s41564-024-01917-1

Clémence Fayt, Nuria Morales-Puerto, Amandine Everard

引用次数: 0

Predicting child health with gut microbiome development trajectories